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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E131K MUTANT OF THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN
 
Authors :  Y. -X. He, Y. Kang, W. J. Zhang, J. Yu, G. Ma, C. -Z. Zhou
Date :  13 Oct 09  (Deposition) - 26 Jan 11  (Release) - 26 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  B
Keywords :  Alpha+Beta Sandwich, Autocatalytic Cleavage, Cell Membrane, Developmental Protein, Disease Mutation, Glycoprotein, Hydrolase, Lipoprotein, Membrane, Palmitate, Protease, Secreted, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. -X. He, Y. Kang, W. J. Zhang, J. Yu, G. Ma, C. -Z. Zhou
Crystal Structure Of The E131K Mutant Of The Indian Hedgeho N-Terminal Signalling Domain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INDIAN HEDGEHOG PROTEIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainROSSETA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentINDIAN HEDGEHOG PROTEIN N-PRODUCT
    GeneIHH
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIHH, HHG-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:145 , ASP B:152 , HIS B:187 , HOH B:305BINDING SITE FOR RESIDUE ZN B 1001
2AC2SOFTWAREHOH B:14 , GLN B:51 , SER B:53 , ARG B:168 , HOH B:287 , HOH B:310 , HOH B:419 , HOH B:463BINDING SITE FOR RESIDUE SO4 B 1
3AC3SOFTWARETYR B:67 , GLY B:69 , LYS B:70 , ARG B:160BINDING SITE FOR RESIDUE SO4 B 2
4AC4SOFTWAREHOH B:13 , ARG B:66 , LYS B:92 , ARG B:128 , THR B:130 , ARG B:158 , HOH B:308 , HOH B:357 , HOH B:459BINDING SITE FOR RESIDUE SO4 B 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K7I)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:53 -Pro B:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_015981P46LIHH_HUMANDisease (ACFD)121917856BP46L
2UniProtVAR_015982E95KIHH_HUMANDisease (BDA1)121917852BE95K
3UniProtVAR_015983D100EIHH_HUMANDisease (BDA1)121917854BD100E
4UniProtVAR_015984D100NIHH_HUMANDisease (BDA1)28936377BD100N
5UniProtVAR_015985E131KIHH_HUMANDisease (BDA1)121917853BK131K
6UniProtVAR_015986V190AIHH_HUMANDisease (ACFD)121917857BV190A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K7I)

(-) Exons   (0, 0)

(no "Exon" information available for 3K7I)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain B from PDB  Type:PROTEIN  Length:157
 aligned with IHH_HUMAN | Q14623 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:157
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       
            IHH_HUMAN    41 PRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSEHSAA 197
               SCOP domains d3k7ib_ B: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains HH_signal-3k7iB02 B:41-189                                                                                                                           --Hint-3 Pfam domains
         Sec.struct. author ...........ee.....................hhhhhhhee.....eee......hhh.eehhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeeee..eeeee........ Sec.struct. author
             SAPs(SNPs) (1) -----L------------------------------------------------K----E------------------------------K----------------------------------------------------------A------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------N------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k7i B  41 PRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTKGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSEHSAA 197
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K7I)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: H-int (15)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (IHH_HUMAN | Q14623)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005113    patched binding    Interacting selectively and non-covalently with the patched (ptc) protein, a receptor for hedgehog proteins.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0007267    cell-cell signaling    Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
    GO:0042733    embryonic digit morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
    GO:0001947    heart looping    The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.
    GO:0016539    intein-mediated protein splicing    The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
    GO:0060135    maternal process involved in female pregnancy    A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0033085    negative regulation of T cell differentiation in thymus    Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation in the thymus.
    GO:0046639    negative regulation of alpha-beta T cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell differentiation.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0033088    negative regulation of immature T cell proliferation in thymus    Any process that stops, prevents, or reduces the frequency, rate or extent of immature T cell proliferation in the thymus.
    GO:0009968    negative regulation of signal transduction    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
    GO:0033089    positive regulation of T cell differentiation in thymus    Any process that activates or increases the frequency, rate or extent of T cell differentiation in the thymus.
    GO:0046638    positive regulation of alpha-beta T cell differentiation    Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation.
    GO:0032332    positive regulation of chondrocyte differentiation    Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0045880    positive regulation of smoothened signaling pathway    Any process that activates or increases the frequency, rate or extent of smoothened signaling.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
    GO:0007224    smoothened signaling pathway    A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
    GO:0061053    somite development    The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IHH_HUMAN | Q146233k7g 3k7h 3k7j 3n1f 3n1m 3n1o 3n1p

(-) Related Entries Specified in the PDB File

3k7g THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN, WILD TYPE
3k7h THE E95K MUTANT OF THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN
3k7j THE D100E MUTANT OF THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN